PATJ

PATJ crumbs cell polarity complex component, the group of MicroRNA protein coding host genes|Crumbs complex|PDZ domain containing

Basic information

Region (hg38): 1:61742477-62178675

Previous symbols: [ "INADL" ]

Links

ENSG00000132849 ∙ NCBI:10207 ∙ OMIM:603199 ∙ HGNC:28881 ∙ Uniprot:Q8NI35 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PATJ gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PATJ gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	4	7
missense			20	2	3	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	20	5	8

Variants in PATJ

This is a list of pathogenic ClinVar variants found in the PATJ region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-61766464-G-T			Uncertain significance (Jan 10, 2024)
1-61769298-T-C		not specified	Uncertain significance (Oct 22, 2021)
1-61775343-A-G			Benign (Dec 31, 2019)
1-61787911-C-A			Likely benign (Jan 01, 2024)
1-61787929-T-C			Benign (Mar 02, 2018)
1-61801625-A-G		not specified	Uncertain significance (Sep 17, 2021)
1-61801719-A-G		not specified	Uncertain significance (Aug 12, 2021)
1-61827453-G-T			Uncertain significance (Aug 10, 2023)
1-61827512-C-T		not specified	Uncertain significance (Aug 17, 2021)
1-61856062-G-T			Likely benign (Jul 01, 2022)
1-61856087-G-A		not specified	Uncertain significance (Jul 26, 2021)
1-61861632-G-C			Benign (May 31, 2017)
1-61864321-A-G			Benign (May 31, 2017)
1-61864462-G-A			Benign (Mar 02, 2018)
1-61875352-C-G		not specified	Likely benign (Jul 20, 2021)
1-61884254-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-61899649-G-A			Likely benign (Nov 01, 2022)
1-61908432-G-T		not specified	Uncertain significance (Nov 15, 2021)
1-61914590-A-G		not specified	Uncertain significance (Sep 17, 2021)
1-61927754-A-G		not specified	Uncertain significance (Nov 12, 2021)
1-62017863-A-G		not specified	Uncertain significance (Sep 22, 2021)
1-62017888-C-G		not specified	Uncertain significance (Sep 27, 2021)
1-62017914-C-T			Benign (Jan 25, 2018)
1-62079574-T-C			Benign (Jan 25, 2018)
1-62108514-A-G		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PATJ	protein_coding	protein_coding	ENST00000371158	42	421444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-50	0.00000626	125236	0	511	125747	0.00203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	854	963	0.887	0.0000500	11711
Missense in Polyphen		338	381.83	0.8852		4581
Synonymous	1.02	336	361	0.932	0.0000203	3530
Loss of Function	1.19	84	96.6	0.870	0.00000519	1173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00264	0.00255
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.00481	0.00474
Finnish	0.00454	0.00454
European (Non-Finnish)	0.00162	0.00160
Middle Eastern	0.00481	0.00474
South Asian	0.00193	0.00186
Other	0.00132	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Scaffolding protein that may bring different proteins into adjacent positions at the cell membrane. May regulate protein targeting, cell polarity and integrity of tight junctions. May regulate the surface expression and/or function of ASIC3 in sensory neurons. May recruit ARHGEF18 to apical cell-cell boundaries (PubMed:22006950). {ECO:0000269|PubMed:11927608, ECO:0000269|PubMed:22006950}.
• Pathway: Tight junction - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Intolerance Scores

• rvis_EVS: 2.27
• rvis_percentile_EVS: 98.24

Haploinsufficiency Scores

• pHI: 0.175
• hipred: Y
• hipred_score: 0.628
• ghis: 0.466

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Patj

Gene ontology

• Biological process: intracellular signal transduction;bicellular tight junction assembly
• Cellular component: centrosome;microtubule organizing center;cytosol;plasma membrane;bicellular tight junction;apical plasma membrane;cell junction;protein-containing complex;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding